Method for treating a semiconductor device

ABSTRACT

A sensor array includes a plurality of sensors. A sensor of the plurality of sensors has a sensor pad exposed at a surface of the sensor array. A method of treating the sensor array includes exposing at least the sensor pad to a wash solution including sulfonic acid and an organic solvent and rinsing the wash solution from the sensor pad.

CROSS-REFERENCE TO RELATED APPLICATION(S)

This application is a divisional of U.S. patent application Ser. No.15/704,695 filed Sep. 14, 2017, now U.S. Pat. No. 10,041,904; which is acontinuation of U.S. Non-Provisional application Ser. No. 14/779,517filed Sep. 23, 2015 (now abandoned), which is a 371 National StageApplication No. of PCT/US2014/032214 filed Mar. 28, 2014, which claimsbenefit of U.S. Provisional Application No. 61/806,603 filed Mar. 29,2013, and U.S. Provisional Application No. 61/817,805 filed Apr. 30,2013, which are all incorporated herein by reference in their entirety.

FIELD OF THE DISCLOSURE

This disclosure, in general, relates to methods for treating sensorarrays, sensor arrays formed by such methods, and solutions for use insuch methods.

BACKGROUND

Arrays of sensors formed in semiconductor substrates are increasinglybeing used in fields such as analytical chemistry and molecular biology.For example, when analytes are captured on or near sensor pads of asensor array, the analytes or byproducts of reactions associated withthe analytes can be detected and used to elucidate information regardingthe analyte. In particular, such sensor arrays have found use in geneticanalysis, such as genetic sequencing or quantitative amplification.

During manufacture, various semiconductor processing techniques canalter the nature of the surface of sensor array and the surface of wellstructures around the sensor array. Such processing can also leaveresidues on the surface. Altered surface chemistry or residues canprevent or limit the capture of analytes proximate to the sensors. Assuch, the effectiveness of such sensor arrays is reduced and signalsresulting from such sensor arrays may include erroneous data or no data.

SUMMARY

In an aspect, a sensor device including a sensor array and optionally awell array corresponding to the sensor array or a cap attached over thesensor array can be treated with a wash solution. The wash solution caninclude an organic solvent and an acid, such as a sulfonic acid, e.g.,alkyl benzene sulfonic acid. The sensor device can be further treatedwith a basic solution, such as a NaOH solution, or can be rinsed with alow boiling organic solvent or water. Optionally, the sensor device canbe dried.

BRIEF DESCRIPTION OF THE DRAWINGS

The present disclosure may be better understood, and its numerousfeatures and advantages made apparent to those skilled in the art byreferencing the accompanying drawings.

FIG. 1 includes an illustration of an exemplary measurement system.

FIG. 2 includes an illustration of an exemplary measurement component.

FIG. 3 includes an illustration of exemplary array of measurementcomponents.

FIG. 4 includes an illustration of exemplary well configurations.

FIG. 5 includes an illustration of exemplary well and sensorconfigurations.

FIG. 6 and FIG. 7 include illustrations of exemplary sensor devices.

FIG. 8, FIG. 9, and FIG. 10 include flow diagrams illustrating exemplarymethods.

FIG. 11 includes an illustration of exemplary methods for preparing asequencing device.

The use of the same reference symbols in different drawings indicatessimilar or identical items.

DETAILED DESCRIPTION

In an exemplary embodiment, a method of treating a sensor array includesapplying a wash solution to the sensor array and rinsing the washsolution from the sensor array. In particular, the wash solutionincludes an organic solvent and an acid, such as a sulfonic acid. Thesulfonic acid can include an alkyl or alkyl aryl sulfonic acid. In anexample, the alkyl or alkyl aryl sulfonic acid can have an alkyl grouphaving between 9 and 18 carbons. For example, the sulfonic acid caninclude dodecyl benzene sulfonic. The organic solvent can be a non-polarsolvent or an aprotic polar solvent. In an example, the organic solventcan have a normal boiling point a range of 65° C. to 275° C. In anexample, the organic solvent includes heptane. In another example, theorganic solvent includes undecane. In an additional example, the organicsolvent includes dimethylformamide, acetonitrile, dimethyl sulfoxide, orcombinations thereof. Following treatment with the wash solution, thesensor array can be rinsed with a rinse solution. In an example, therinse solution includes a low boiling organic solvent such as alcohol,for example, ethanol or isopropanol. In another example, the rinsesolution can include water. The method may further include applying abasic solution or a weak acid solution following application of the washsolution and before rinsing. The basic solution can have a pH of atleast 7, such as at least 8, and can include a strong base, such assodium hydroxide. In an example, the wash solution and the basicsolution can be applied repeatedly, such as 2 or more times, 3 or moretimes or even 4 or more times, but generally not greater than 10 times.

In a particular embodiment, a wash solution is applied to at least asensor pad of the sensor array. The sensor array can include a pluralityof sensors. A sensor of the sensor array can include a sensor pad.Optionally, a well structure can be defined over the sensor array andinclude a plurality of wells correspond with sensor pads of the sensorarray. A well of the well array can expose a sensor pad of a sensor.Optionally, a cap including at least one fluid port can be disposed orattached over the sensor array and the well structure. A space for fluidcan be defined between the cap and the well structure or sensor arrayand can be in fluid communication with the fluid port of the cap. Thewash solution can be applied through the fluid port and into the spacebetween the cap and the well structure. Optionally, a basic solution canbe applied through the fluid port to the space between the cap and thewell structure following application of the wash solution. Applicationof the wash solution followed by the basic solution can be repeated,such as at least twice or even at least 3 times. A rinse solution can beapplied through the fluid port, for example, including alcohol or water.Optionally, the system can be dried.

In another exemplary embodiment, a sensor array includes a plurality ofsensors. A sensor of the plurality of sensors includes a sensor pad. Awell structure is disposed over the sensor array and includes a wellarray that operatively corresponds with the sensor array. A well of thewell array exposes a sensor pad of a sensor. The wash solution includingan acid, such as a sulfonic acid, and an organic solvent can be appliedto the sensor array for a period between 30 seconds and 30 min. Thesensor array can be rinsed with a rinse solution. In an example, therinse solution can include a low boiling organic solvent such as analcohol. The sensor array can be rinsed one or more times with the lowboiling organic solvent. In another example or in addition, the sensorarray can be rinsed with water, such as deionized water. The sensorarray can be dried and a cap can be attached over the well structure andthe sensor array. The cap can include at least one fluid port. A spaceis defined between the cap and the sensor array or the well structureand is in fluid communication with the fluid port.

In a particular embodiment, a sensor system includes a flow cell inwhich a sensory array is disposed, includes communication circuitry inelectronic communication with the sensory array, and includes containersand fluid controls in fluidic communication with the flow cell. In anexample, FIG. 1 illustrates an expanded and cross-sectional view of aflow cell 100 and illustrates a portion of a flow chamber 106. A reagentflow 108 flows across a surface of a well array 102, in which thereagent flow 108 flows over the open ends of wells of the well array102. The well array 102 and a sensor array 105 together can form anintegrated unit forming a lower wall (or floor) of flow cell 100. Areference electrode 104 can be fluidically coupled to flow chamber 106.Further, a flow cell cover 130 encapsulates flow chamber 106 to containreagent flow 108 within a confined region.

FIG. 2 illustrates an expanded view of a well 201 and a sensor 214, asillustrated at 110 of FIG. 1. The volume, shape, aspect ratio (such asbase width-to-well depth ratio), and other dimensional characteristicsof the wells can be selected based on the nature of the reaction takingplace, as well as the reagents, byproducts, or labeling techniques (ifany) that are employed. The sensor 214 can be a chemical field-effecttransistor (chemFET), more specifically an ion-sensitive FET (ISFET),with a floating gate 218 having a sensor plate 220 optionally separatedfrom the well interior by a material layer 216. In addition, aconductive layer (not illustrated) can be disposed over the sensor plate220. In an example, the material layer 216 includes an ion sensitivematerial layer. The material layer 216 can be a ceramic layer, such asan oxide of zirconium, hafnium, tantalum, aluminum, or titanium, amongothers, or a nitride of titanium. In an example, the material layer 216can have a thickness in a range of 5 nm to 100 nm, such as a range of 10nm to 70 nm, a range of 15 nm to 65 nm, or even a range of 20 nm to 50nm. Together, the sensor plate 220 and the material layer 216 form asensor pad.

While the material layer 216 is illustrated as extending beyond thebounds of the illustrated FET component, the material layer 216 canextend along the bottom of the well 201 and optionally along the wallsof the well 201. The sensor 214 can be responsive to (and generate anoutput signal related to) the amount of a charge 224 present on materiallayer 216 opposite the sensor plate 220. Changes in the charge 224 cancause changes in a current between a source 221 and a drain 222 of thechemFET. In turn, the chemFET can be used directly to provide acurrent-based output signal or indirectly with additional circuitry toprovide a voltage-based output signal. Reactants, wash solutions, andother reagents can move in and out of the wells by a diffusion mechanism240.

In an embodiment, reactions carried out in the well 201 can beanalytical reactions to identify or determine characteristics orproperties of an analyte of interest. Such reactions can generatedirectly or indirectly byproducts that affect the amount of chargeadjacent to the sensor plate 220. If such byproducts are produced insmall amounts or rapidly decay or react with other constituents,multiple copies of the same analyte can be analyzed in the well 201 atthe same time in order to increase the output signal generated. In anembodiment, multiple copies of an analyte can be attached to a solidphase support 212, either before or after deposition into the well 201.In an example, the solid phase support 212 can be a particle, such as apolymeric particle or an inorganic particle. In another example, thesolid phase support 212 can be a polymer matrix, such as a hydrophilicpolymer matrix, for example, a hydrogel matrix or the like.

The well 201 can be defined by a wall structure, which can be formed ofone or more layers of material. In an example, the wall structure canhave a thickness extending from the lower surface to the upper surfaceof the well in a range of 0.01 micrometers to 10 micrometers, such as arange of 0.05 micrometers to 10 micrometers, a range of 0.1 micrometersto 10 micrometers, a range of 0.3 micrometers to 10 micrometers, or arange of 0.5 micrometers to 6 micrometers. In particular, the thicknesscan be in a range of 0.01 micrometers to 1 micrometer, such as a rangeof 0.05 micrometers to 0.5 micrometers, or a range of 0.05 micrometersto 0.3 micrometers. The wells 201 can have a characteristic diameter,defined as the square root of 4 times the cross-sectional area (A)divided by Pi (e.g., sqrt(4*A/π), of not greater than 5 micrometers,such as not greater than 3.5 micrometers, not greater than 2.0micrometers, not greater than 1.6 micrometers, not greater than 1.0micrometers, not greater than 0.8 micrometers or even not greater than0.6 micrometers. In an example, the wells 201 can have a characteristicdiameter of at least 0.01 micrometers.

While FIG. 2 illustrates a single-layer wall structure and asingle-layer material layer 216, the system can include one or more wallstructure layers, one or more conductive layers or one or more materiallayers. For example, the wall structure can be formed of one or morelayers, including an oxide of silicon or TEOS or including a nitride ofsilicon.

In a particular example illustrated in FIG. 3, a system 300 includes awell wall structure 302 defining an array of wells 304 disposed over oroperatively coupled to sensor pads of a sensor array. The well wallstructure 302 defines an upper surface 306. A lower surface 308associated with the well is disposed over a sensor pad of the sensorarray. The well wall structure 302 defines a sidewall 310 between theupper surface 306 and the lower surface 308. As described above, amaterial layer in contact with sensor pads of the sensor array canextend along the lower surface 308 of a well of the array of wells 304or along at least a portion of the wall 310 defined by the well wallstructure 302. The upper surface 306 can be free of the material layer.In particular, a polymer matrix can be disposed in the wells of thearray of wells 304. The upper surface 306 can be substantially free ofthe polymer matrix. For example, the upper surface 306 can include anarea that is free of the polymer matrix, such as at least 70% of thetotal area, at least 80% of the total area, at least 90% of the totalarea or approximately 100% of the total area.

While the wall surface of FIG. 2 is illustrated as extendingsubstantially vertically and outwardly, the wall surface can extend invarious directions and have various shapes. Substantially verticallydenotes extending in a direction having a component that is normal tothe surface defined by the sensor pad. For example, as illustrated inFIG. 4, a well wall 402 can extend vertically, being parallel to anormal component 412 of a surface defined by a sensor pad. In anotherexample, the wall surface 404 extends substantially vertically, in anoutward direction away from the sensor pad, providing a larger openingto the well than the area of the lower surface of the well. Asillustrated in FIG. 4, the wall surface 404 extends in a directionhaving a vertical component parallel to the normal component 412 of thesurface 414. In an alternative example, a wall surface 406 extendssubstantially vertically in an inward direction, providing an openingarea that is smaller than an area of the lower surface of the well. Thewall surface 406 extends in a direction having a component parallel tothe normal component 412 of the surface 414.

While the surfaces 402, 404, or 406 are illustrated by straight lines,some semiconductor or CMOS manufacturing processes can result instructures having nonlinear shapes. In particular, wall surfaces, suchas wall surface 408 and upper surfaces, such as upper surface 410, canbe arcuate in shape or take various nonlinear forms. While thestructures and devices illustrated herewith are depicted as havinglinear layers, surfaces, or shapes, actual layers, surfaces, or shapesresulting from semiconductor processing can differ to some degree,possibly including nonlinear and arcuate variations of the illustratedembodiment.

FIG. 5 includes an illustration of exemplary wells including ionsensitive material layers. For example, a well structure 502 can definean array of wells, such as exemplary wells 504, 506, or 508. The wells(504, 506, or 508) can be operatively coupled to an underlying sensor(not illustrated) or linked to such an underlying sensor. Exemplary well504 includes an ion sensitive material layer 510 defining the bottom ofthe well 504 and extending into the structure 502. While not illustratedin FIG. 5, a conductive layer, such as a gate, for example, a floatinggate of ion sensitive field effect transistor can reside below the ionsensitive material layer 510.

In another example, as illustrated by well 506, an ion sensitivematerial layer 512 can define the bottom of the well 506 withoutextending into the structure 502. In a further example, a well 508 caninclude an ion sensitive layer 514 that extends along at least a portionof a sidewall 516 of the well 508 defined by the structure 502. Asabove, the ion sensitive material layers 512 or 514 can reside overconductive layers or gates of underlying electronic devices.

As illustrated in FIG. 6, the sensor device can include a sensor array602 formed within a semiconductor substrate. A well structure is definedover the sensor array. A cap 604 is attached to the well structure orthe sensor array 602. For example, the cap 604 can be adhered to thesensor array or well structure 602 using an adhesive. The cap 604includes fluid ports 606 or 608, which are in fluid communication with aflow cell 610 defined between the cap 604 and the sensor array and wellarray 602. Fluid applied to one of the fluid ports 606 or 608 can flowthrough the flow cell 610 and optionally out the other port 608 or 606.In another example illustrated in FIG. 7, a cap 702 can include fluidports 704 and 706 and can define a larger flow space. The cap can beadhered over a well array or sensor array, for example, using anadhesive.

As illustrated in the method 800 of FIG. 8, a sensor array can beexposed to a wash solution including an acid, such as sulfonic acid,phosphonic acid, or a combination thereof, as illustrated 802. The washsolution can further include an organic solvent.

An exemplary sulfonic acid includes an alkyl sulfonic acid, an alkylaryl sulfonic acid, or a combination thereof. An exemplary alkylsulfonic acid includes an alkyl group having 1 to 18 carbons, such as 1to 14 carbons, 1 to 10 carbons, or 1 to 5 carbons. In another example,the alkyl group of the alkyl sulfonic acid has 10 to 14 carbons. Forexample, an alkyl sulfonic acid can include methanesulfonic acid,ethanesulfonic acid, propane sulfonic acid, butane sulfonic acid, orcombinations thereof. In another example, the alkyl group can befunctionalized, for example, with a terminal functional group oppositethe sulfonic acid functional group. An exemplary functionalized alkylsulfonic acid includes an alkyl sulfonic acid functionalized with aterminal amine group, such as taurine. In a further example, the alkylgroups of the sulfonic acid can be halogenated, such as fluorinated.

In a further example, the sulfonic acid includes an alkyl aryl sulfonicacid. The alkyl aryl sulfonic acid, for example, alkyl benzene sulfonicacid, can include an alkyl group having between 1 and 20 carbons. Forexample, the alkyl group can have between 9 and 18 carbons, such asbetween 10 and 14 carbons. In a particular example, the alkyl arylsulfonic acid includes dodecyl benzene sulfonic acid. The dodecylbenzene sulfonic acid can be a purified form of dodecyl benzene sulfonicacid having at least 90%, such as at least 95% of alkyl aryl sulfonicacid having an alkyl group with 12 carbons. Alternatively, the dodecylbenzene sulfonic acid can include a blend of alkyl benzene sulfonic acidhaving alkyl groups with an average of 12 carbons. The alkyl arylsulfonic acid can be alkylated at a blend of positions along the alkylchain. In another example, the alkyl group can have between 1 and 6carbons. For example, the alkyl aryl sulfonic acid can include toluenesulfonic acid.

The wash solution can have a concentration between 10 mM and 500 mMacid, such as sulfonic acid. For example, the wash solution can have aconcentration between 50 mM and 250 mM acid. In another example, thewash solution includes between 0.5 wt % and 25 wt % of the acid, such assulfonic acid. For example, the wash solution can include between 1 wt %and 10 wt % of the acid, such as sulfonic acid, such as between 2.5 wt %and 5 wt % of the acid, such as sulfonic acid.

The organic solvent within the wash solution is a non-aqueous solventproviding solubility for the acid (e.g., sulfonic acid) to at least theconcentrations above. In an example, the organic solvent can be aprotic.The organic solvent can be a non-polar organic solvent. In anotherexample, the organic solvent can be a polar aprotic solvent. In anexample, the organic solvent can have a normal boiling point in a rangeof 36° C. to 345° C. For example, the normal boiling point can be in arange of 65° C. to 275° C. In another example, the normal boiling pointcan be in a range of 65° C. to 150° C. Alternatively, the normal boilingpoint is in a range of 150° C. to 220° C.

In a particular example, the non-polar organic solvent includes analkane solvent, an aromatic solvent, or a combination thereof. An alkanesolvent can have between 6 and 20 carbons. For example, the alkane canhave between 6 and 14 carbons, such as between 6 and 9 carbons.Alternatively, the alkane can have between 10 and 14 carbons. In aparticular example, the alkane is a linear alkane. For example, thealkane solvent can include pentane, hexane, heptanes, octane, decane,undecane, dodecane, or combinations thereof. In another example, thealkane is halogenated. An exemplary branched alkane can includehydrogenated dimers of C11 or C12 alpha olefins.

In a further example, the organic solvent can include a polar aproticsolvent. For example, the polar aprotic solvent can includetetrahydrofuran, ethylacetate, acetone, dimethylformamide, acetonitrile,dimethyl sulfoxide, N-methyl pyrrolidone (NMP), or combinations thereof.In another example, the organic solvent may be free of ether solventsand, for example, may include dimethylformamide, acetonitrile, dimethylsulfoxide, or combinations thereof.

As illustrated at 804, the wash solution and sensor device can be heatedwhile the sensor pad is exposed to wash solution. In an example, thewash solution and the sensor device can be heated at a temperature in arange of 35° C. to 60° C. For example, the temperature can be in a rangeof 40° C. to 50° C.

As illustrated 806, the sensor array can be exposed to the wash solutionand optionally heated for a period in a range of 30 seconds to 30 min.For example, the period can be in a range of 30 seconds to 10 min., suchas a range of 30 seconds to 5 min., or even a range of 1 min. to 2 min.

An organic solvent or water can be used to rinse the sensor array, asillustrated 808, following exposure to the wash solution. The organicsolvent can be a low boiling organic solvent. An exemplary low boilingorganic solvent can have a normal boiling point range of 25° C. to 100°C., such as a normal boiling point in a range of 50° C. to 100° C. In anexample, the low boiling organic solvent includes an alcohol, such asethanol or propanol. Alternatively, the organic solvent can be N-methylpyrrolidone (NMP). Alternatively or in addition, the sensor array can berinsed with water, such as deionized water. In a particular example, theorganic solvent is at least partially miscible with water and theorganic solvent of the acid/solvent mixture.

As illustrated at 810, the sensor array can be dried. In an example, thesensor array can be dried under an inert atmosphere, such as using drynitrogen or helium. In another example, the sensor can be heated under adry atmosphere. In a further example, the sensor array can be driedunder vacuum.

In a further example illustrated in FIG. 9, a method 900 includesexposing a sensor array to a wash solution including an acid asdescribed above, for example, sulfonic acid, as illustrated 902. Asensor device can include the sensor array and optionally a wellstructure defining a well array operatively corresponding to the sensorarray. A well of the well array can expose a sensor pad of a sensor ofthe sensor array. The wash solution can have the composition describedabove. Optionally, the sensor array and the wash solution can be heatedas illustrated 904. For example, the sensor array and the wash solutioncan be heated to temperatures described above.

In a further example, the sensor array can be exposed to the washsolution and optionally heated for a period in a range of 30 seconds to30 min., as illustrated 906. Alternatively, the sensor array can beexposed to a wash solution and optionally heated for the time periodsdescribed above.

Following exposure to the wash solution, the sensor array can be rinsedwith a solvent, e.g., a low boiling solvent, as illustrated 908.Exemplary low boiling solvents are described above. Alternatively, thesolvent can be N-methyl pyrrolidone (NMP). The sensor array can berinsed with the low boiling solvent one time or more than one time.

Following rinsing with the low boiling organic solvent, the sensor arraycan be rinsed with water, such as deionized water, as illustrated at910. Following rinsing with water, the sensor array can be dried asillustrated 912. For example, the sensor array can be exposed to drynitrogen gas.

Once dried, a cap can be applied over the sensor array, as illustrated914. For example, the cap can be attached to the sensor array or anintervening well structure using an adhesive. In particular, the capincludes fluid ports in fluid communication with a space defined betweenthe cap and a well structure over the sensor array. Optionally, themethod can be applied to a wafer prior to separating the wafer intoarrays and capping individual arrays.

In a further exemplary embodiment illustrated in FIG. 10, a method 1000includes exposing a sensor array to a wash solution that includes acidas described above, for example, sulfonic acid, as illustrated at 1002.The wash solution can further include an organic solvent. In particular,the sensor array can include a well structure defining an array of wellsoperatively corresponding to the array of sensors. A sensor pad of asensor is exposed by a well of the well array. A cap can be attachedover the sensor array or the well array. The cap includes fluid ports incommunication with a space defined between the cap and the well array orsensor array. The wash solution can be applied through the fluid portinto the space. The composition of a wash solution can be as describedabove.

Optionally, as illustrated at 1004, the wash solution and the sensorarray can be heated. For example, the wash solution and the sensor arraycan be heated at the temperatures described above.

The sensor array can be exposed to the wash solution and optionallyheated for a first period, as illustrated at 1006. The first period canhave a range of 30 seconds to 30 min., such as the ranges of timesperiods described above.

In addition, a basic solution can be applied to the sensor array for asecond period, as illustrated at 1008. For example, the basic solutioncan be applied through a fluid port of a cap and into the space definedbetween the cap and the well structure or sensor array. The basicsolution has a pH greater than 7, such as a pH greater than 8, or even apH greater than 9. The basic solution includes a strong base, such assodium or potassium hydroxide or a tetraalkyl ammonium hydroxide, suchas tetramethyl ammonium hydroxide or tetraethyl ammonium hydroxide. Thebase is in a concentration between 0.05 M and 1.5 M. For example, thebase can be in a concentration between 0.05 M and 1.0 M, such as between0.05 M and 0.5 M. The sensor array can be exposed to the basic solutionfor a period of between 20 seconds and 15 min., such as a period ofbetween 20 seconds and 5 min or a period of between 30 seconds and 2min. Alternatively, a weak acid solution can be substituted for thebasic solution.

The sensor array can be exposed to the wash solution followed byexposure to the basic solution r or the weak acid repeatedly, such as ktimes. For example, k can be 1, 2, or 3, but generally is not greaterthan 10.

Following exposure to the wash solution and the basic solution, thesensor array can be rinsed with the organic solvent or water, asillustrated at 1010. Exemplary low boiling organic solvents includethose described above. Alternatively, the organic solvent can beN-methyl pyrrolidone (NMP). The sensor array can be rinsed with lowboiling organic solvents one or more times followed by a rinse withwater. Optionally, the sensor array can be dried, such as with exposureto dry nitrogen, as illustrated at 1012.

The method of FIG. 10 can alternatively be applied to a wafer includingmultiple arrays. The wafer can be separated into individual arrays andcaps applied to the individual arrays following drying the wafer.

Such treatment of sensor arrays has been shown to improve loading ofpolymeric beads that incorporating an analyte and secure the analyte inproximity to sensor pads of the sensor array. In particular, suchtreatment improves loading of polymeric beads that includepolynucleotide analytes amplified thereon. For example, such treatmentmethods improve the performance of sequence sequencing devices. Suchtreatment of sensor arrays has been shown to improve sensor signal andsignal-to-noise ratio (SNR), particularly in FET-based sensor arrays.

For example, FIG. 11 illustrates and exemplary sequencing systemenhanced by the above described treatment methods. In a particularexample illustrated in FIG. 11, polymeric particles can be used as asupport for polynucleotides during sequencing techniques. For example,such hydrophilic particles can immobilize a polynucleotide forsequencing using fluorescent sequencing techniques. In another example,the hydrophilic particles can immobilize a plurality of copies of apolynucleotide for sequencing using ion-sensing techniques.Alternatively, the above described treatments can improve polymer matrixbonding to a surface of a sensor array. The polymer matrices can captureanalytes, such as polynucleotides for sequencing.

In general, the polymeric particle can be treated to include abiomolecule, including nucleosides, nucleotides, nucleic acids(oligonucleotides and polynucleotides), polypeptides, saccharides,polysaccharides, lipids, or derivatives or analogs thereof. For example,a polymeric particle can bind or attach to a biomolecule. A terminal endor any internal portion of a biomolecule can bind or attach to apolymeric particle. A polymeric particle can bind or attach to abiomolecule using linking chemistries. A linking chemistry includescovalent or non-covalent bonds, including an ionic bond, hydrogen bond,affinity bond, dipole-dipole bond, van der Waals bond, and hydrophobicbond. A linking chemistry includes affinity between binding partners,for example between: an avidin moiety and a biotin moiety; an antigenicepitope and an antibody or immunologically reactive fragment thereof; anantibody and a hapten; a digoxigen moiety and an anti-digoxigenantibody; a fluorescein moiety and an anti-fluorescein antibody; anoperator and a repressor; a nuclease and a nucleotide; a lectin and apolysaccharide; a steroid and a steroid-binding protein; an activecompound and an active compound receptor; a hormone and a hormonereceptor; an enzyme and a substrate; an immunoglobulin and protein A; oran oligonucleotide or polynucleotide and its corresponding complement.

As illustrated in FIG. 11, a plurality of polymeric particles 1104 canbe placed in a solution along with a plurality of polynucleotides 1102.The plurality of particles 1104 can be activated or otherwise preparedto bind with the polynucleotides 1102. For example, the particles 1104can include an oligonucleotide complementary to a portion of apolynucleotide of the plurality of polynucleotides 1102. In anotherexample, the polymeric particles 1104 can be modified with targetpolynucleotides 1104 using techniques such as biotin-streptavidinbinding.

In a particular embodiment, the hydrophilic particles andpolynucleotides are subjected to polymerase chain reaction (PCR)amplification or recombinase polymerase amplification (RPA). Forexample, dispersed phase droplets 1106 or 1108 are formed as part of anemulsion and can include a hydrophilic particle or a polynucleotide. Inan example, the polynucleotides 1102 and the hydrophilic particles 1104are provided in low concentrations and ratios relative to each othersuch that a single polynucleotide 1102 is likely to reside within thesame dispersed phase droplets as a single hydrophilic particle 1104.Other droplets, such as a droplet 1108, can include a single hydrophilicparticle and no polynucleotide. Each droplet 1106 or 1108 can includeenzymes, nucleotides, salts or other components sufficient to facilitateduplication of the polynucleotide.

In a particular embodiment, an enzyme such as a polymerase is present,bound to, or is in close proximity to the hydrophilic particle orhydrogel particle of the dispersed phase droplet. In an example, apolymerase is present in the dispersed phase droplet to facilitateduplication of the polynucleotide. A variety of nucleic acid polymerasemay be used in the methods described herein. In an exemplary embodiment,the polymerase can include an enzyme, fragment or subunit thereof, whichcan catalyze duplication of the polynucleotide. In another embodiment,the polymerase can be a naturally-occurring polymerase, recombinantpolymerase, mutant polymerase, variant polymerase, fusion or otherwiseengineered polymerase, chemically modified polymerase, syntheticmolecules, or analog, derivative or fragment thereof.

Following PCR or RPA, particles are formed, such as particle 1110, whichcan include the hydrophilic particle 1112 and a plurality of copies 1114of the polynucleotide. While the polynucleotides 1114 are illustrated asbeing on a surface of the particle 1110, the polynucleotides can extendwithin the particle 1110. Hydrogel and hydrophilic particles having alow concentration of polymer relative to water can includepolynucleotide segments on the interior of and throughout the particle1110 or polynucleotides can reside in pores and other openings. Inparticular, the particle 1110 can permit diffusion of enzymes,nucleotides, primers and reaction products used to monitor the reaction.A high number of polynucleotides per particle produces a better signal.

In embodiments, polymeric particles from an emulsion-breaking procedurecan be collected and washed in preparation for sequencing. Collectioncan be conducted by contacting biotin moieties (e.g., linked toamplified polynucleotide templates which are attached to the polymericparticles) with avidin moieties, and separation away from polymericparticles lacking biotinylated templates. Collected polymeric particlesthat carry double-stranded template polynucleotides can be denatured toyield single-stranded template polynucleotides for sequencing.Denaturation steps can include treatment with base (e.g., NaOH),formamide, or pyrrolidone.

In an exemplary embodiment, the particle 1110 can be utilized in asequencing device. For example, a sequencing device 1116 can include anarray of wells 1118. The sequencing device 1116 can be treated with awash solution including sulfonic acid, as described above. A particle1110 can be placed within a well 1118.

In an example, a primer can be added to the wells 1118 or the particle1110 can be pre-exposed to the primer prior to placement in the well1118. In particular, the particle 1110 can include bound primer. Theprimer and polynucleotide form a nucleic acid duplex including thepolynucleotide (e.g., a template nucleic acid) hybridized to the primer.The nucleic acid duplex is an at least partially double-strandedpolynucleotide. Enzymes and nucleotides can be provided to the well 1118to facilitate detectible reactions, such as nucleotide incorporation.

Sequencing can be performed by detecting nucleotide addition. Nucleotideaddition can be detected using methods such as fluorescent emissionmethods or ion detection methods. For example, a set of fluorescentlylabeled nucleotides can be provided to the system 1116 and can migrateto the well 1118. Excitation energy can be also provided to the well1118. When a nucleotide is captured by a polymerase and added to the endof an extending primer, a label of the nucleotide can fluoresce,indicating which type of nucleotide is added.

In an alternative example, solutions including a single type ofnucleotide can be fed sequentially. In response to nucleotide addition,the pH within the local environment of the well 1118 can change. Such achange in pH can be detected by ion sensitive field effect transistors(ISFET). As such, a change in pH can be used to generate a signalindicating the order of nucleotides complementary to the polynucleotideof the particle 1110.

In particular, a sequencing system can include a well, or a plurality ofwells, disposed over a sensor pad of an ionic sensor, such as a fieldeffect transistor (FET). In embodiments, a system includes one or morepolymeric particles loaded into a well which is disposed over a sensorpad of an ionic sensor (e.g., FET), or one or more polymeric particlesloaded into a plurality of wells which are disposed over sensor pads ofionic sensors (e.g., FET). In embodiments, an FET can be a chemFET or anISFET. A “chemFET” or chemical field-effect transistor, includes a typeof field effect transistor that acts as a chemical sensor. The chemFEThas the structural analog of a MOSFET transistor, where the charge onthe gate electrode is applied by a chemical process. An “ISFET” orion-sensitive field-effect transistor, can be used for measuring ionconcentrations in solution; when the ion concentration (such as H+)changes, the current through the transistor changes accordingly.

In embodiments, the FET may be a FET array. As used herein, an “array”is a planar arrangement of elements such as sensors or wells. The arraymay be one or two dimensional. A one dimensional array can be an arrayhaving one column (or row) of elements in the first dimension and aplurality of columns (or rows) in the second dimension. The number ofcolumns (or rows) in the first and second dimensions may or may not bethe same. The FET or array can comprise 10², 10³, 10⁴, 10⁵, 10⁶, 10⁷ ormore FETs.

In embodiments, one or more microfluidic structures can be fabricatedabove the FET sensor array to provide for containment or confinement ofa biological or chemical reaction. For example, in one implementation,the microfluidic structure(s) can be configured as one or more wells (ormicrowells, or reaction chambers, or reaction wells, as the terms areused interchangeably herein) disposed above one or more sensors of thearray, such that the one or more sensors over which a given well isdisposed detect and measure analyte presence, level, or concentration inthe given well. In embodiments, there can be a 1:1 correspondence of FETsensors and reaction wells.

Returning to FIG. 11, in another example, a well 1118 of the array ofwells can be operatively connected to measuring devices. For example,for fluorescent emission methods, a well 1118 can be operatively coupledto a light detection device. In the case of ionic detection, the lowersurface of the well 1118 may be disposed over a sensor pad of an ionicsensor, such as a field effect transistor.

One exemplary system involving sequencing via detection of ionicbyproducts of nucleotide incorporation is the Ion Torrent PGM™ orProton™ sequencer (Life Technologies), which is an ion-based sequencingsystem that sequences nucleic acid templates by detecting hydrogen ionsproduced as a byproduct of nucleotide incorporation. Typically, hydrogenions are released as byproducts of nucleotide incorporations occurringduring template-dependent nucleic acid synthesis by a polymerase. TheIon Torrent PGM™ or Proton™ sequencer detects the nucleotideincorporations by detecting the hydrogen ion byproducts of thenucleotide incorporations. The Ion Torrent PGM™ or Proton™ sequencer caninclude a plurality of template polynucleotides to be sequenced, eachtemplate disposed within a respective sequencing reaction well in anarray. The wells of the array can each be coupled to at least one ionsensor that can detect the release of H+ ions or changes in solution pHproduced as a byproduct of nucleotide incorporation. The ion sensorcomprises a field effect transistor (FET) coupled to an ion-sensitivedetection layer that can sense the presence of H+ ions or changes insolution pH. The ion sensor can provide output signals indicative ofnucleotide incorporation which can be represented as voltage changeswhose magnitude correlates with the H+ ion concentration in a respectivewell or reaction chamber. Different nucleotide types can be flowedserially into the reaction chamber, and can be incorporated by thepolymerase into an extending primer (or polymerization site) in an orderdetermined by the sequence of the template. Each nucleotideincorporation can be accompanied by the release of H+ ions in thereaction well, along with a concomitant change in the localized pH. Therelease of H+ ions can be registered by the FET of the sensor, whichproduces signals indicating the occurrence of the nucleotideincorporation. Nucleotides that are not incorporated during a particularnucleotide flow may not produce signals. The amplitude of the signalsfrom the FET can also be correlated with the number of nucleotides of aparticular type incorporated into the extending nucleic acid moleculethereby permitting homopolymer regions to be resolved. Thus, during arun of the sequencer multiple nucleotide flows into the reaction chamberalong with incorporation monitoring across a multiplicity of wells orreaction chambers can permit the instrument to resolve the sequence ofmany nucleic acid templates simultaneously.

In a first aspect, a sensor array includes a plurality of sensors. Asensor of the plurality of sensors has a sensor pad exposed at a surfaceof the sensor array. A method of treating the sensor array includesexposing at least the sensor pad to a wash solution including acid andan organic solvent and rinsing the wash solution from the sensor pad.

In a second aspect, a sensor array includes a plurality of sensors. Asensor of the plurality of the sensors includes a sensor pad. A wellstructure defines a well array corresponding with the sensor array. Awell of the well array exposes the sensor pad. A cap is attached overthe sensor array and the well structure and includes a fluid port. Aspace is defined between the cap and the well structure. A method oftreating the sensor array includes applying a wash solution through thefluid port into the space and waiting for a first period between 30seconds and 30 minutes. The wash solution includes acid and an organicsolvent. The method further includes applying a basic solution throughthe fluid port into the space and waiting for a second period between 20seconds and 15 minutes and applying a rinse solution through the fluidport. In an example of the second aspect, the method further includesrepeating applying the wash solution and applying the basic solution.

In a third aspect, a sensor array includes a plurality of sensors. Asensor of the plurality of sensors includes a sensor pad. A wellstructure defines a well array corresponding with the sensor array. Awell of the well array exposes the sensor pad. A method of treating thesensor array includes applying a wash solution to at least the sensorpad and waiting for a first period between 30 seconds and 30 minutes.The wash solution includes acid and an organic solvent. The methodfurther includes rinsing at least the sensor pad with a low boilingorganic solvent and drying the sensor array. In an example of the thirdaspect, the method further includes rinsing with water following rinsingwith the low boiling organic solvent and prior to drying. In anotherexample of the third aspect and the above examples, the method furtherincludes attaching a cap over the sensor array and the well array, thecap including a fluid port, a space defined between the cap and the wellarray in fluid communication with the fluid port.

In an example of the first, second, and third aspects and the aboveexamples, the acid includes a sulfonic acid. The sulfonic acid caninclude an alkyl sulfonic acid, alkyl aryl sulfonic acid, or acombination thereof. In an example, the alkyl aryl sulfonic acidincludes an alkyl group having between 1 and 20 carbons. For example,the alkyl group has between 9 and 18 carbons, such as between 10 and 14carbons. In another example, the alkyl group has between 1 and 6carbons.

In another example of the first, second, and third aspects and the aboveexamples, the sulfonic acid includes dodecyl benzene sulfonic acid. In afurther example of the first, second, and third aspects and the aboveexamples, the sulfonic acid includes methanesulfonic acid,ethanesulfonic acid, propane sulfonic acid, butane sulfonic acid, orcombinations thereof. In an additional example of the first, second, andthird aspects and the above examples, the sulfonic acid includes paratoluene sulfonic acid.

In a further example of the first, second, and third aspects and theabove examples, the wash solution includes between 10 mM and 500 mM ofthe acid. For example, the wash solution includes between 50 mM and 250mM of the acid.

In an additional example of the first, second, and third aspects and theabove examples, the wash solution includes between 0.5 wt % and 25 wt %of the acid. For example, the wash solution includes between 1 wt % and10 wt % of the acid, such as between 2.5 wt % and 5 wt % of the acid.

In another example of the first, second, and third aspects and the aboveexamples, the organic solvent is non-polar.

In a further example of the first, second, and third aspects and theabove examples, the organic solvent has a normal boiling point in arange of 36° C. to 345° C. For example, the normal boiling point is in arange of 65° C. to 275° C. In an example, the normal boiling point is ina range of 65° C. to 150° C. In an alternative example, the normalboiling point is in a range of 150° C. to 220° C.

In an additional example of the first, second, and third aspects and theabove examples, the organic solvent is an alkane having between 6 and 24carbons. For example, the alkane has between 6 and 14 carbons, such asbetween 6 and 9 carbons or alternatively, between 10 and 14 carbons.

In a further example of the first, second, and third aspects and theabove examples, the organic solvent is an aprotic polar solvent. Forexample, the polar aprotic solvent includes tetrahydrofuran,ethylacetate, acetone, dimethylformamide, acetonitrile, dimethylsulfoxide, N-methyl pyrrolidone (NMP), or combinations thereof.

In another example of the first, second, and third aspects and the aboveexamples, the method further includes heating the sensor pad and thewash solution while exposing the sensor pad to the wash solution. Forexample, heating includes heating at a temperature in a range of 35° C.to 70° C. For example, the temperature is in a range of 40° C. to 55° C.

In a further example of the first, second, and third aspects and theabove examples, exposing includes exposing for a period in a range of 30seconds to 30 minutes. For example, the period is in a range of 30seconds to 10 minutes, such as in a range of 30 seconds to 5 minutes orin a range of 1 minute to 3 minutes.

In an additional example of the first, second, and third aspects and theabove examples, the method further includes exposing at least the sensorpad to a basic solution. For example, the basic solution includesbetween 0.005 M and 1.5 M sodium hydroxide, such as between 0.01 M and1.0 M sodium hydroxide or between 0.01 M and 0.5 M sodium hydroxide. Inan additional example, exposing at least the sensor pad to the basicsolution occurs following exposing the sensor pad to the wash solution.The method can further includes repeating exposing at least the sensorpad to the wash solution and exposing at least the sensor pad to thebasic solution.

In another example of the first, second, and third aspects and the aboveexamples, rinsing includes rinsing with a low boiling organic solventhaving a normal boiling point in a range of 25° C. to 100° C. Forexample, the low boiling organic solvent has a normal boiling point in arange of 50° C. to 100° C. In a particular example, the low boilingorganic solvent includes alcohol. For example, the alcohol includesethanol or isopropanol.

In a further example of the first, second, and third aspects and theabove examples, rinsing includes rinsing with water.

In a fourth aspect, a system includes a sensor device treated by themethod of any one of the above aspects and examples.

In a fifth aspect, a solution includes 2.5 wt % to 5 wt % sulfonic acidand a non-polar linear alkane having between 6 and 18 carbons.

In a sixth aspect, a kit includes a nucleotide solution including atleast one nucleotide type, polymeric particles, and a wash solutionincluding 0.5 wt % to 20 wt % sulfonic acid and an organic solventhaving a normal boiling point in a range of 65° C. to 275° C.

Note that not all of the activities described above in the generaldescription or the examples are required, that a portion of a specificactivity may not be required, and that one or more further activitiesmay be performed in addition to those described. Still further, theorder in which activities are listed are not necessarily the order inwhich they are performed.

Particular salts of above described acids or bases can have activity,and may be useful in the above described methods. Salts include alkalior alkali earth metal salts, or tetraalkylammonium salts of the aboveacids or bases.

In the foregoing specification, the concepts have been described withreference to specific embodiments. However, one of ordinary skill in theart appreciates that various modifications and changes can be madewithout departing from the scope of the invention as set forth in theclaims below. Accordingly, the specification and figures are to beregarded in an illustrative rather than a restrictive sense, and allsuch modifications are intended to be included within the scope ofinvention.

As used herein, the terms “comprises,” “comprising,” “includes,”“including,” “has,” “having” or any other variation thereof, areintended to cover a non-exclusive inclusion. For example, a process,method, article, or apparatus that comprises a list of features is notnecessarily limited only to those features but may include otherfeatures not expressly listed or inherent to such process, method,article, or apparatus. Further, unless expressly stated to the contrary,“or” refers to an inclusive-or and not to an exclusive-or. For example,a condition A or B is satisfied by any one of the following: A is true(or present) and B is false (or not present), A is false (or notpresent) and B is true (or present), and both A and B are true (orpresent).

Also, the use of “a” or “an” are employed to describe elements andcomponents described herein. This is done merely for convenience and togive a general sense of the scope of the invention. This descriptionshould be read to include one or at least one and the singular alsoincludes the plural unless it is obvious that it is meant otherwise.

Benefits, other advantages, and solutions to problems have beendescribed above with regard to specific embodiments. However, thebenefits, advantages, solutions to problems, and any feature(s) that maycause any benefit, advantage, or solution to occur or become morepronounced are not to be construed as a critical, required, or essentialfeature of any or all the claims.

After reading the specification, skilled artisans will appreciate thatcertain features are, for clarity, described herein in the context ofseparate embodiments, may also be provided in combination in a singleembodiment. Conversely, various features that are, for brevity,described in the context of a single embodiment, may also be providedseparately or in any subcombination. Further, references to valuesstated in ranges include each and every value within that range.

What is claimed is:
 1. A method of treating a sensor array, the sensorarray including a plurality of sensors, a sensor of the plurality of thesensors including a sensor pad, a well structure defining a well arrayhaving a plurality of wells, a well of the plurality of wells disposedover each sensor of the sensor array and providing an opening to thesensor pad, the method comprising: applying a wash solution to the welland at least the sensor pad and waiting for a first period between 30seconds and 30 minutes, the wash solution including an acid and anorganic solvent, wherein the organic solvent is selected from the groupconsisting of non-polar and polar aprotic organic solvents; rinsing atleast the sensor pad with an alcohol having a normal boiling point in arange of 25° C. to 100° C.; and drying the sensor array.
 2. The methodof claim 1, further comprising rinsing with water following rinsing withthe alcohol and prior to drying.
 3. The method of claim 1, furthercomprising attaching a cap over the sensor array and the well array, thecap including a fluid port, a space defined between the cap and the wellarray in fluid communication with the fluid port.
 4. The method of claim1, wherein the acid includes sulfonic acid.
 5. The method of claim 1,wherein the acid includes dodecyl benzene sulfonic acid.
 6. The methodof claim 1, wherein the acid includes para toluene sulfonic acid.
 7. Themethod of claim 1, wherein the wash solution includes between 10 mM and500 mM of the acid.
 8. The method of claim 1, wherein the organicsolvent has a normal boiling point in a range of 36° C. to 345° C. 9.The method of claim 1, wherein the organic solvent is a non-polarorganic solvent comprising an alkane having between 6 and 24 carbons.10. The method of claim 1, wherein the polar aprotic solvent includestetrahydrofuran, ethylacetate, acetone, dimethylformamide, acetonitrile,dimethyl sulfoxide, N-methyl pyrrolidone, or combinations thereof. 11.The method of claim 1, further comprising heating the sensor pad and thewash solution while exposing the sensor pad to the wash solution at atemperature in a range of 35° C. to 70° C.
 12. The method of claim 1,further comprising exposing at least the sensor pad to a basic solutionfollowing exposing the sensor pad to the wash solution.
 13. The methodof claim 1, wherein rinsing includes rinsing with the alcohol having anormal boiling point in a range of 50° C. to 100° C.
 14. The method ofclaim 4, wherein the sulfonic acid includes alkyl sulfonic acid, alkylaryl sulfonic acid, or a combination thereof.
 15. The method of claim14, wherein the alkyl aryl sulfonic acid includes an alkyl group havingbetween 1 and 20 carbons.
 16. The method of claim 15, wherein the alkylgroup has between 9 and 18 carbons.
 17. The method of claim 15, whereinthe alkyl group has between 1 and 6 carbons.